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<p>MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.  
 <a href="classmoltk_1_1MatrixScorer__.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="MatrixScorer_8hpp_source.html">MatrixScorer.hpp</a>&gt;</code></p>
<div class="dynheader">
Collaboration diagram for moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;:</div>
<div class="dyncontent">
<div class="center"><img src="classmoltk_1_1MatrixScorer____coll__graph.png" border="0" usemap="#moltk_1_1MatrixScorer___3_01SCORE__TYPE_00_01GAP__NSEGS_01_4_coll__map" alt="Collaboration graph"/></div>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1MatrixScorer__-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a093911098a3e0b7ad665a0cf2a5c6447">MatrixScorer_</a> (const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt; &amp;<a class="el" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">matrix</a>)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a MatrixScorer using a particular substitution matrix.  <a href="#a093911098a3e0b7ad665a0cf2a5c6447"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a08105eea98536c8b5766d1b2f6a9b145">create_positions</a> (std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt; * &gt; &amp;positions, const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;alignment) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create precached data structures for alignment of two individual sequences.  <a href="#a08105eea98536c8b5766d1b2f6a9b145"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a6d0e8213f712b0fe14b6b82f472c17be">create_positions</a> (std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt; * &gt; &amp;positions, const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;alignment) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create precached data structures for alignment of two alignments.  <a href="#a6d0e8213f712b0fe14b6b82f472c17be"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a0d7def4e72c6e4263cb9506a1055978b">get_end_gaps_free</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#abe3caf1c15a2e325c7bd942b38fa8295">set_end_gaps_free</a> (bool f)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a74e1d7a6961120ce14f0097b88907514">get_default_gap_open_score</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Alignment score reduction for initiating an alignment gap.  <a href="#a74e1d7a6961120ce14f0097b88907514"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a6dce77af635e8e89b12eb632f88371f2">set_default_gap_open_score</a> (SCORE_TYPE score)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Set alignment score reduction for initiating an alignment gap.  <a href="#a6dce77af635e8e89b12eb632f88371f2"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#ad4f161927c9c6f2491b345c24a120ac7">get_default_gap_extension_score</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Alignment score reduction for increasing the length of an alignment gap by one position.  <a href="#ad4f161927c9c6f2491b345c24a120ac7"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#ae7fdb188444d50d14267783fd3bcba88">set_default_gap_extension_score</a> (SCORE_TYPE score)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Set Alignment score reduction for increasing the length of an alignment gap by one position.  <a href="#ae7fdb188444d50d14267783fd3bcba88"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7">score</a> (char residue1, char residue2) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Look up score of two residue one-letter-codes in the matrix.  <a href="#ab90650541e6f63c72b6a20a1480b2de7"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#adbe9a587fd12d874ebe5edcdc9531d6d">calc_explicit_sum_of_pairs_score</a> (const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&lt; SCORE_TYPE &gt; &amp;alignment) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Inefficient computation of sum-of-pairs score, for use in testing and debugging.  <a href="#adbe9a587fd12d874ebe5edcdc9531d6d"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a6369337ff8f5877031de76db62c2c3bf">calc_explicit_pair_score</a> (int i, int j, const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&lt; SCORE_TYPE &gt; &amp;alignment) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Compute pair score between two sequences in an alignment.  <a href="#a6369337ff8f5877031de76db62c2c3bf"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">b_end_gaps_free</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">default_gap_open_score</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">default_gap_extension_score</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">matrix</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><h3>template&lt;class SCORE_TYPE, int GAP_NSEGS&gt;<br/>
class moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</h3>

<p>MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="a093911098a3e0b7ad665a0cf2a5c6447"></a><!-- doxytag: member="moltk::MatrixScorer_::MatrixScorer_" ref="a093911098a3e0b7ad665a0cf2a5c6447" args="(const moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt; &amp;matrix)" -->
<div class="memitem">
<div class="memproto">
<div class="memtemplate">
template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::<a class="el" href="classmoltk_1_1MatrixScorer__.html">MatrixScorer_</a> </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt; &amp;&#160;</td>
          <td class="paramname"><em>matrix</em></td><td>)</td>
          <td><code> [explicit]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Create a MatrixScorer using a particular substitution matrix. </p>

</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a6369337ff8f5877031de76db62c2c3bf"></a><!-- doxytag: member="moltk::MatrixScorer_::calc_explicit_pair_score" ref="a6369337ff8f5877031de76db62c2c3bf" args="(int i, int j, const Alignment_&lt; SCORE_TYPE &gt; &amp;alignment) const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::calc_explicit_pair_score </td>
          <td>(</td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>i</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int&#160;</td>
          <td class="paramname"><em>j</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&lt; SCORE_TYPE &gt; &amp;&#160;</td>
          <td class="paramname"><em>alignment</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Compute pair score between two sequences in an alignment. </p>

</div>
</div>
<a class="anchor" id="adbe9a587fd12d874ebe5edcdc9531d6d"></a><!-- doxytag: member="moltk::MatrixScorer_::calc_explicit_sum_of_pairs_score" ref="adbe9a587fd12d874ebe5edcdc9531d6d" args="(const Alignment_&lt; SCORE_TYPE &gt; &amp;alignment) const " -->
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<div class="memtemplate">
template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::calc_explicit_sum_of_pairs_score </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&lt; SCORE_TYPE &gt; &amp;&#160;</td>
          <td class="paramname"><em>alignment</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Inefficient computation of sum-of-pairs score, for use in testing and debugging. </p>

</div>
</div>
<a class="anchor" id="a08105eea98536c8b5766d1b2f6a9b145"></a><!-- doxytag: member="moltk::MatrixScorer_::create_positions" ref="a08105eea98536c8b5766d1b2f6a9b145" args="(std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt; * &gt; &amp;positions, const Alignment &amp;alignment) const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">void <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::create_positions </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt; * &gt; &amp;&#160;</td>
          <td class="paramname"><em>positions</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;&#160;</td>
          <td class="paramname"><em>alignment</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Create precached data structures for alignment of two individual sequences. </p>

</div>
</div>
<a class="anchor" id="a6d0e8213f712b0fe14b6b82f472c17be"></a><!-- doxytag: member="moltk::MatrixScorer_::create_positions" ref="a6d0e8213f712b0fe14b6b82f472c17be" args="(std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt; * &gt; &amp;positions, const Alignment &amp;alignment) const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
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          <td class="memname">void <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::create_positions </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt; * &gt; &amp;&#160;</td>
          <td class="paramname"><em>positions</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="namespacemoltk.html#a2d7910ca714d56deeca1e4219cd80721">Alignment</a> &amp;&#160;</td>
          <td class="paramname"><em>alignment</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Create precached data structures for alignment of two alignments. </p>

</div>
</div>
<a class="anchor" id="ad4f161927c9c6f2491b345c24a120ac7"></a><!-- doxytag: member="moltk::MatrixScorer_::get_default_gap_extension_score" ref="ad4f161927c9c6f2491b345c24a120ac7" args="() const " -->
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<div class="memproto">
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::get_default_gap_extension_score </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Alignment score reduction for increasing the length of an alignment gap by one position. </p>

</div>
</div>
<a class="anchor" id="a74e1d7a6961120ce14f0097b88907514"></a><!-- doxytag: member="moltk::MatrixScorer_::get_default_gap_open_score" ref="a74e1d7a6961120ce14f0097b88907514" args="() const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::get_default_gap_open_score </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Alignment score reduction for initiating an alignment gap. </p>

</div>
</div>
<a class="anchor" id="a0d7def4e72c6e4263cb9506a1055978b"></a><!-- doxytag: member="moltk::MatrixScorer_::get_end_gaps_free" ref="a0d7def4e72c6e4263cb9506a1055978b" args="() const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
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          <td class="memname">bool <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::get_end_gaps_free </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
        </tr>
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<a class="anchor" id="ab90650541e6f63c72b6a20a1480b2de7"></a><!-- doxytag: member="moltk::MatrixScorer_::score" ref="ab90650541e6f63c72b6a20a1480b2de7" args="(char residue1, char residue2) const " -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
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          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::score </td>
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          <td class="paramname"><em>residue1</em>, </td>
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          <td class="paramkey"></td>
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          <td>)</td>
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<p>Look up score of two residue one-letter-codes in the matrix. </p>

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<a class="anchor" id="ae7fdb188444d50d14267783fd3bcba88"></a><!-- doxytag: member="moltk::MatrixScorer_::set_default_gap_extension_score" ref="ae7fdb188444d50d14267783fd3bcba88" args="(SCORE_TYPE score)" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
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          <td class="memname">void <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::set_default_gap_extension_score </td>
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<p>Set Alignment score reduction for increasing the length of an alignment gap by one position. </p>

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<a class="anchor" id="a6dce77af635e8e89b12eb632f88371f2"></a><!-- doxytag: member="moltk::MatrixScorer_::set_default_gap_open_score" ref="a6dce77af635e8e89b12eb632f88371f2" args="(SCORE_TYPE score)" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
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          <td class="memname">void <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::set_default_gap_open_score </td>
          <td>(</td>
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<p>Set alignment score reduction for initiating an alignment gap. </p>

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<a class="anchor" id="abe3caf1c15a2e325c7bd942b38fa8295"></a><!-- doxytag: member="moltk::MatrixScorer_::set_end_gaps_free" ref="abe3caf1c15a2e325c7bd942b38fa8295" args="(bool f)" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a69dc9913654f395b8a6912cd5866edc7"></a><!-- doxytag: member="moltk::MatrixScorer_::b_end_gaps_free" ref="a69dc9913654f395b8a6912cd5866edc7" args="" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
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          <td class="memname">bool <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::<a class="el" href="classmoltk_1_1MatrixScorer__.html#a69dc9913654f395b8a6912cd5866edc7">b_end_gaps_free</a><code> [protected]</code></td>
        </tr>
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<div class="memdoc">

</div>
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<a class="anchor" id="ae46f2161ce2413aa901cfe80d79b4ac3"></a><!-- doxytag: member="moltk::MatrixScorer_::default_gap_extension_score" ref="ae46f2161ce2413aa901cfe80d79b4ac3" args="" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::<a class="el" href="classmoltk_1_1MatrixScorer__.html#ae46f2161ce2413aa901cfe80d79b4ac3">default_gap_extension_score</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
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<a class="anchor" id="aa6e2fb51837602663ca39a4ba1b9fa3f"></a><!-- doxytag: member="moltk::MatrixScorer_::default_gap_open_score" ref="aa6e2fb51837602663ca39a4ba1b9fa3f" args="" -->
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<div class="memtemplate">
template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">SCORE_TYPE <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::<a class="el" href="classmoltk_1_1MatrixScorer__.html#aa6e2fb51837602663ca39a4ba1b9fa3f">default_gap_open_score</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
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<a class="anchor" id="a4bf1242ff86ad47455d09ce4df1a18e7"></a><!-- doxytag: member="moltk::MatrixScorer_::matrix" ref="a4bf1242ff86ad47455d09ce4df1a18e7" args="" -->
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template&lt;class SCORE_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
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          <td class="memname"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a>&lt;SCORE_TYPE&gt; <a class="el" href="classmoltk_1_1MatrixScorer__.html">moltk::MatrixScorer_</a>&lt; SCORE_TYPE, GAP_NSEGS &gt;::<a class="el" href="classmoltk_1_1MatrixScorer__.html#a4bf1242ff86ad47455d09ce4df1a18e7">matrix</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="MatrixScorer_8hpp_source.html">MatrixScorer.hpp</a></li>
</ul>
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